Expression Of Protein-coding Genes Research Articles

Fibronectin Modulates the Expression of miRNAs in Prostate Cancer Cell Lines.

Prostate cancer (PCa) is a significant cause of cancer-related deaths among men and companion animals, such as dogs. However, despite its high mortality and incidence rates, the molecular mechanisms underlying this disease remain to be fully elucidated. Among the many factors involved in prostate carcinogenesis, the extracellular matrix (ECM) plays a crucial role. This ECM in the prostate is composed mainly of collagen fibers, reticular fibers, elastic fibers, proteoglycans and glycoproteins, such as fibronectin. Fibronectin is a glycoprotein whose dysregulation has been implicated in the development of multiple types of cancer, and it has been associated with cell migration, invasion, and metastasis. Furthermore, our research group has previously shown that fibronectin induces transcriptional changes by modulating the expression of protein coding genes in LNCaP cells. However, potential changes at the post-transcriptional level are still not well understood. This study investigated the impact of exposure to fibronectin on the expression of a key class of regulatory RNAs, the microRNAs (miRNAs), in prostate cancer cell lines LNCaP and PC-3. Five mammalian miRNAs (miR-21, miR-29b, miR-125b, miR-221, and miR-222) were differentially expressed after fibronectin exposure in prostate cell lines. The expression profile of hundreds of mRNAs predicted to be targeted by these miRNAs was analyzed using publicly available RNA-Sequencing data (GSE64025, GSE68645, GSE29155). Also, protein-protein interaction networks and enrichment analysis were performed to gain insights into miRNA biological functions. Altogether, these functional analyzes revealed that fibronectin exposure impacts the expression of miRNAs potentially involved in PCa causing changes in critical signaling pathways such as PI3K-AKT, and response to cell division, death, proliferation, and migration. The relationship here demonstrated between fibronectin exposure and altered miRNA expression improves the comprehension of PCa in both men and other animals, such as dogs, which naturally develop prostate cancer.

DNA Methylome and LncRNAome Analysis Provide Insights Into Mechanisms of Genome-Dosage Effects in Autotetraploid Cassava.

Whole genome duplication (WGD) increases the dosage of all coding and non-coding genes, yet the molecular implications of genome-dosage effects remain elusive. In this study, we generated integrated maps of the methylomes and lncRNAomes for diploid and artificially generated autotetraploid cassava (Manihot esculenta Crantz). We found that transposable elements (TEs) suppressed adjacent protein coding gene (PCG)-expression levels, while TEs activated the expression of nearby long non-coding RNAs (lncRNAs) in the cassava genome. The hypermethylation of DNA transposons in mCG and mCHH sites may be an effective way to suppress the expression of nearby PCGs in autotetraploid cassava, resulting in similar expression levels for most of PCGs between autotetraploid and diploid cassava. In the autotetraploid, decreased methylation levels of retrotransposons at mCHG and mCHH sites contributed to reduced methylation of Gypsy-neighboring long intergenic non-coding RNAs, potentially preserving diploid-like expression patterns in the major of lncRNAs. Collectively, our study highlighted that WGD-induced DNA methylation variation in DNA transposons and retrotransposons may be as direct adaptive responses to dosage of all coding-genes and lncRNAs, respectively.

RiceNCexp: a rice non-coding RNA co-expression atlas based on massive RNA-seq and small-RNA seq data.

Non-coding RNAs (ncRNAs) play important roles in regulating expression of protein-coding genes. Although gene expression databases have emerged in a timely manner, a comprehensive expression database for ncRNAs is still lacking. Herein, we constructed a rice ncRNA co-expression atlas (RiceNCexp), based on 491 RNA-seq and 274 small RNA (sRNA)-seq datasets. RiceNCexp hosts four types of ncRNAs, namely lncRNAs, PHAS genes, miRNAs, and phasiRNAs. RiceNCexp provides comprehensive expression information for rice ncRNAs in 22 tissues/organs, an efficient tau-based mining tool for tissue-specific ncRNAs, and the robust co-expression analysis among ncRNAs or between ncRNAs and protein-coding genes, based on 116 pairs of RNA-seq and sRNA-seq libraries from the same experiments. In summary, RiceNCexp is a user-friendly and comprehensive rice ncRNA co-expression atlas and can be freely accessed at https://cbi.njau.edu.cn/RiceNCexp/.

High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes.

The advent of massively parallel sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long noncoding RNAs (lncRNAs). Selected functional examples raised the possibility that lncRNAs, as a class, may maintain broad regulatory roles. Expression of lncRNAs is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory functions. A more detailed understanding of these regulatory roles may be obtained through careful examination of the precise timing of lncRNA expression relative to adjacent protein-coding genes. Despite the diversity of reported lncRNA regulatory mechanisms, where causal cis-regulatory relationships exist, lncRNA transcription is expected to precede changes in target gene expression. Using a high temporal resolution RNA-seq time course, we profiled the expression dynamics of several thousand lncRNAs and protein-coding genes in synchronized, transitioning human cells. Our findings reveal that lncRNAs are expressed synchronously with adjacent protein-coding genes. Analysis of lipopolysaccharide-activated mouse dendritic cells revealed the same temporal relationship observed in transitioning human cells. Our findings suggest broad-scale cis-regulatory roles for lncRNAs are not common. The strong association between lncRNAs and adjacent genes may instead indicate an origin as transcriptional by-products from active protein-coding gene promoters and enhancers.

P729: DEREGULATION OF NONCODING RNAS DERIVED FROM KDM GENES IS ASSOCIATED WITH AZACITIDINE RESPONSE IN PATIENTS WITH MYELODYSPLASTIC SYNDROMES AND ACUTE MYELOID LEUKEMIA

Background: Prediction of response to azacitidine (AZA) treatment is an important challenge in the management of higher-risk myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). To date, no clinical, cytogenetic, or molecular markers of AZA treatment outcome have been validated to support clinical decisions. Moreover, little is known about how AZA efficiency can be affected by various noncoding RNAs (ncRNAs), such as long ncRNAs (lncRNAs) and circular RNAs (circRNAs). KDM genes encode demethylases of histone lysine residues (e.g., KDM1 mediates demethylation of H3K4 and H3K9, and KDM4 acts on H3K9, H3K36, and H1K26). KDMs are often differentially expressed in leukemia and they cooperate with transcription factors to activate or repress gene expression. Aims: Our aims were to provide biological insight into the contribution of ncRNAs to AZA mechanisms of action and to propose novel disease biomarkers that would be able to predict future response to AZA treatment. Based on our results, we particularly focused on expression and function of KDM-related ncRNAs. Methods: Whole transcriptome RNA sequencing (RNA-seq) was performed in CD34+ bone marrow cells from 26 patients with MDS or AML with myelodysplasia-related changes (AML-MRC) before AZA treatment (11 responders and 16 nonresponders), and 9 healthy controls. Expression of protein coding genes (PCGs), lncRNAs and circRNAs was bioinformatically processed. Results: Overall, differential expression analysis between AZA responders and nonresponders identified significant deregulation of 202 PCGs, 34 lncRNAs, and 21 circRNAs. Surprisingly, machine learning data showed that predictive potential of ncRNAs was stronger than that of PCGs. Within the data, deregulation of several KDM-related ncRNAs was observed, e.g., CTC-482H14.5 (antisense RNA to KDM4B gene, downregulated in AZA responders), hsa_circ_0003889 (circRNA processed from KDM1A, downregulated in AZA responders), and hsa_circ_0001580 (circRNA processed from KDM1B, upregulated in AZA responders). By contrast with these noncoding transcripts, the levels of corresponding PCGs (namely KDM1A/1B/4B) were not altered between AZA responders and nonresponders, suggesting that the deregulated ncRNAs play specific roles independent of their host genes. Further, the best predictor genes were defined by machine learning using RNA-seq data and pathway analysis linked these markers to cellular processes related to MDS/AML. Interestingly, CTC-482H14.5 was identified as one of the strongest predictors of AZA treatment response. Expression of this KDM-related ncRNA was coregulated with expression of DNMT1, EZH2, and multiple MCM genes, associating this transcript with epigenetic regulation and recombinational repair pathways. Summary/Conclusion: Several ncRNAs processed from KDM genes seem to be closely related to the responsiveness of MDS/AML-MRC patients to AZA treatment. In this study, novel functions were predicted for these ncRNAs, pointing to possible mechanisms by which their deregulation could affect AZA treatment response. Acknowledgements: Supported by GA CR (No. 20-19162S) and MH CZ-DRO (UHKT, 00023736).

P595: DISCOVERY OF NOVEL CIRCULAR RNAS (CIRCRNAS) OF THE APOPTOSIS-RELATED BAX AND BCL2L12 GENES WITH A MULTIFACETED ROLE IN CHRONIC LYMPHOCYTIC LEUKEMIA, USING CUTTING-EDGE NANOPORE SEQUENCING TECHNOLOGY

Background: Circular RNAs (circRNAs), a novel RNA type generated by back-splicing, are key indirect regulators of gene expression, with deregulated expression and established involvement in several human malignancies. Many circRNAs have been shown to bind microRNAs (miRNAs), thus making miRNAs unavailable to regulate protein-coding gene expression. Moreover, some of them have been described to interact with chromatin and affecting its structure. Despite their pivotal roles in the development and progression of cancer, only three studies have investigated their expression and role(s) in chronic lymphocytic leukemia (CLL), so far. The products of BCL2 and its homologues, including BAX and BCL2-like 12 (BCL2L12), are implicated in CLL, as apoptosis regulators. Moreover, expression levels of both BAX and BCL2L12 mRNAs are deregulated in CLL and are associated with patients’ response to therapy and overall survival. However, to the best of our knowledge, nothing is known about circRNAs produced by these two genes and their regulatory potential. Aims: We sought to further elucidate the contribution of both BAX and BCL2L12 in CLL by unraveling the identity of their circRNAs in a B-cell leukemic cell line (EHEB) and by studying in silico their potential interactions with miRNAs having an already established role in CLL. Methods: EHEB cells were propagated according to ATCC instructions. After total RNA extraction, 2μg of total RNA were reverse-transcribed using random hexamers. Next, nested PCR with divergent primers was performed, starting from each exon of BAX and BCL2L12 genes; thus, only cDNAs from BAX and BCL2L12 circRNAs were amplified, respectively. After having mixed and purified all nested-PCR products, nanopore sequencing libraries were built according to an optimized protocol. Following nanopore sequencing and basecalling in a MinION Mk1C 3rd-generation sequencer, sequencing reads were aligned and corrected using Minimap2 and TranscriptClean, respectively. circRNA sequences were identified using an in-house–built, PERL-based algorithm. A single-molecule resolution fluorescent in situ hybridization (FISH) method called circFISH was used to visualize the circRNA distribution in the cells. Lastly, miRDB was used to predict interactions of the most abundant BAX and BCL2L12 circRNAs with miRNAs. Results: We discovered 18 and 21 novel circRNAs produced by BAX and BCL2L12 genes, respectively, in this leukemic cell line. The exon structure of these novel circRNAs showed remarkable diversity, also comprising genomic regions that have previously been considered as intronic, as they are not included in messenger RNAs (mRNAs). Interestingly, one of the two most abundant BAX circRNAs is composed of a single exon, also spanning two introns. Similar intron retentions have been observed in a few BCL2L12 circRNAs. The gamut of miRNAs predicted to be bound by novel circRNAs includes miR-484, miR-181a-2-3p and miR-214-3p. Particularly, the inhibition of miR-214-3p is associated with elevated apoptosis in leukemic B-cells. Summary/Conclusion: Alternative splicing and back-splicing mechanisms of the primary BAX and BCL2L12 transcripts produce multiple distinct circRNAs in this B-cell CLL cell line. Interestingly, one of the two most abundant circular transcripts of BAX is a circRNA spanning three exons and two intervening introns of this gene. Lastly, several miRNAs are predicted to be sequestered by circRNAs of either of these apoptosis-related genes, including miR-181 family members that have been associated with chemosensitivity. Our data suggest a multifaceted role of BAX and BCL2L12 circRNAs in B-cell CLL.

Effects of a High Glycemic Diet and Soluble Epoxide Hydrolase Inhibitor on Hippocampal Microvascular Function, and Multigenomic Modifications

ObjectivesDiet is a modifiable risk factor for cardiovascular disease (CVD) and dementia, yet relatively little is known about the effect of a high glycemic diet (HGD) on the brain microvasculature. The objective of our study was to determine the multigenomic effects of a HGD on hippocampal microvessels, and to determine if a soluble epoxide hydrolase (sEH) inhibitor (sEHI), known to be vasculoprotective and anti-inflammatory, modulates these effects.MethodsWild type male and female mice were fed a low glycemic diet (LGD, 12% sucrose/weight) or a HGD (34% sucrose/weight) with/without the sEHI, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-benzoic acid (t-AUCB), for 12 wks. Brain hippocampal microvascular gene expression was assessed by microarray and data analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors.ResultsGlobal hippocampal microvascular gene expression was fundamentally different for mice fed the HGD vs the LGD. The HGD modulated expression of genes involved in cell signaling, neurodegeneration, metabolism, and cell adhesion/inflammation/oxidation effects reversible by t-AUCB and hence sEH inhibitor correlated with protection against Alzheimer's dementia. However, in female, HGD had very minor genomic modifications, while sEHI presented significant effect in female mice on LGD.ConclusionsOurs is the first study to demonstrate that high dietary glycemia contributes to brain hippocampal microvascular inflammation, through sEH, effects that were sex-dependant.Funding SourcesThis work was supported by an award from the Richard A. and Nora Eccles Foundation (A20-0111), the Richard A. and Nora Eccles Harrison Endowed Chair in Diabetes Research (J.C.R.), and the Frances Lazda Endowed Chair in Women's Cardiovascular Medicine (A.C.V).

Epicatechin Mitigates Anxiety-Related Behavior in a Mouse Model of Obesity by Modulating Gut Microbiome Composition and Global Gene Expression Profile in the Hippocampus

ObjectivesEpicatechin (EC) is a flavan-3-ol abundant in cocoa, apples, and tea, and can prevent vascular dysfunction and development of diseases, such as cardiovascular or neurodegenerative diseases. We have recently shown that EC can prevent lipid-induced brain endothelial cell dysfunction by modulating the expression of protein-coding and non-coding genes (miRNAs, long non-coding RNAs). The aim of our study is to investigate the capacity of EC to mitigate the adverse effects of high-fat diet (HFD) on cognitive function, the gut microbiota dysbiosis, metabolic and inflammatory markers as well as to decipher the molecular mechanisms of EC action. MethodsHealthy eight-weeks old male mice were fed for 24 weeks either: A) a control diet containing 10% total calories from fat; B) a HFD containing 45% total calories from fat; or c) a HFD supplemented with EC (20 mg/kg BW). Plasma metabolic parameters, cognitive tests (open field test, novel object recognition test, Morris water maze), gut microbiota profile (16S sequencing), and genomic modifications (Affymetrix arrays) in the hippocampus followed by in-depth bioinformatic analyses were performed. ResultsEC supplementation resulted in amelioration of HFD-induced increase in plasma glucose and insulin, mitigated anxiety-related behaviors and modulated affected the microbiota composition by affecting abundance of 139 taxa. Transcriptomic analysis demonstrated that EC induced significant changes in the hippocampal gene expression of mice fed with the HFD. We observed changes in expression of 1001 genes corresponding to protein-coding genes, 241 miRNAs, and 167 long non-coding RNAs. The PCA and heatmap analysis revealed opposite expression of genes obtained following EC supplementation when compared to the gene expression profile obtained after consumption of the HFD. Functionality analysis revealed that the differentially expressed gene regulate processes involved in neurofunction, inflammation, cell-cell adhesion, and cell signaling. ConclusionsIn summary, EC supplementation mitigated anxiety-related behavior in a model of diet-induced obesity in mice, which can be in part mediated through the modulation of gut microbiota and by reversing HFD-induced complex genomic modification in the hippocampus. Funding SourcesNIH grants R01DK090492 and R01DK095359. France-Barkley foundation.

The critical role of histone modifications in lung adenocarcinoma based on novel molecular subtypes.

e20510 Background: Studies revealed the pathogenesis and exploring the treatment of lung adenocarcinoma (LUAD), but overall survival (OS) of LUAD patients still remains low in the recent years. Methods: This study analyzed the relationship between gene expression and histone modifications, and discussed the prognostic value of these findings in patients with LUAD. Four types of histone modifications including H3K9me3, H3K27me3, H3K27ac and H3K4me3 were included. Promoters and enhancers in protein coding genes (PCGs) were selected as targeted analyzing regions. Unsupervised consensus clustering was performed to identify molecular subtypes. Cox regression analysis and stepwise Akaike information criterion (stepAIC) were applied to construct a prognostic model. Results: A large number of epigenetic abnormal genes in lung adenocarcinoma were found by comparing the histone modifications and methylation regions on the elements including. We identified 699 epigenetic dysregulated genes specific to LUAD. Finally, based on these epi-PCGs, we constructed three molecular types of LUAD and identified 5 epi-PCGs as prognostic markers for LUAD patients. Conclusions: Our research provided a better understanding that the abnormal epigenetic regulation of PCG expression contributes a lot for the progress of gene regulation in LUAD. These novel molecular subtypes and the prognostic model could serve as guiders to assist decision-makings for LUAD treatment.

From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala).

Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, the system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into "zombies". Despite all these amazing traits, there is no genomic and transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: externa and main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for both P. reticulata and Rhizocephala. Based on the results obtained, the spatial heterogeneity of protein-coding genes expression in different regions of P. reticulata adult female body was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans "got stuck in the metamorphosis", even in their reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of this amazing parasites.

Identifying common transcriptome signatures of cancer by interpreting deep learning models

BackgroundCancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute to oncogenesis vary widely between tumor types, but common gene signatures that relate to core cancer pathways have also been identified. It is not clear, however, whether there exist additional sets of genes or transcriptomic features that are less well known in cancer biology but that are also commonly deregulated across several cancer types.ResultsHere, we agnostically identify transcriptomic features that are commonly shared between cancer types using 13,461 RNA-seq samples from 19 normal tissue types and 18 solid tumor types to train three feed-forward neural networks, based either on protein-coding gene expression, lncRNA expression, or splice junction use, to distinguish between normal and tumor samples. All three models recognize transcriptome signatures that are consistent across tumors. Analysis of attribution values extracted from our models reveals that genes that are commonly altered in cancer by expression or splicing variations are under strong evolutionary and selective constraints. Importantly, we find that genes composing our cancer transcriptome signatures are not frequently affected by mutations or genomic alterations and that their functions differ widely from the genes genetically associated with cancer.ConclusionsOur results highlighted that deregulation of RNA-processing genes and aberrant splicing are pervasive features on which core cancer pathways might converge across a large array of solid tumor types.

Relationship of TP53 gene with retroelements in urogenital organs carcinogenesis

The article presents a hypothesis about the influence of TP53 gene on the development of prostate, kidney, and bladder cancer through negative regulation of retrotransposons. The p53 protein is a transcription factor that controls the expression of various protein-coding genes. The promoter regions of endogenous retroviruses contain almost ideal binding sites for p53, which suppresses translation of these elements and LINE1s. The TP53 gene contains retrotransposons, which promote mutations due to recombinations. Germinal mutations of the TP53 gene in Li–Fraumeni syndrome cause a deficiency of the p53 protein, which leads to the activation of retroelements, which, in turn, cause loss of heterozygosity of the second TP53 allele. The result is a “vicious circle” that stimulates genomic instability and carcinogenesis. This mechanism is possible for sporadic urogenital system malignant neoplasms development, where TP53 mutations are most often identified, acting as drivers of carcinogenesis. At the same time, pathological activation of retroelements is found in many malignant neoplasms. Moreover, the “vicious circle”, when a deficiency of an oncosuppressor causes activation of retroelements that contribute to inactivation of other oncosuppressors, is characteristic not only for р53. Retroelements can be controlled by other oncosuppressor genes that contain hot spots of insertional mutagenesis and retrotransposons (which contribute to recombination events). I suppose that pathological interregulation of retroelements and tumor suppressors is a universal mechanism of carcinogenesis in the development of sporadic malignant neoplasms and hereditary tumor syndromes. Chromoplexy observed in 90 % of prostate cancer samples may reflect these events, since activated retroelements in carcinogenesis contribute to complex chromosomal rearrangements.

FoQDE2-dependent milRNA promotes Fusarium oxysporum f. sp. cubense virulence by silencing a glycosyl hydrolase coding gene expression.

MicroRNAs (miRNAs) are small non-coding RNAs that regulate protein-coding gene expression primarily found in plants and animals. Fungi produce microRNA-like RNAs (milRNAs) that are structurally similar to miRNAs and functionally important in various biological processes. The fungus Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of Banana Fusarium vascular wilt that threatens global banana production. It remains uncharacterized about the biosynthesis and functions of milRNAs in Foc. In this study, we investigated the biological function of milRNAs contributing to Foc pathogenesis. Within 24 hours post infecting the host, the Argonaute coding gene FoQDE2, and two Dicer coding genes FoDCL1 and FoDCL2, all of which are involved in milRNA biosynthesis, were significantly induced. FoQDE2 deletion mutant exhibited decreased virulence, suggesting the involvement of milRNA biosynthesis in the Foc pathogenesis. By small RNA sequencing, we identified 364 small RNA-producing loci in the Foc genome, 25 of which were significantly down-regulated in the FoQDE2 deletion mutant, from which milR-87 was verified as a FoQDE2-depedent milRNA based on qRT-PCR and Northern blot analysis. Compared to the wild-type, the deletion mutant of milR-87 was significantly reduced in virulence, while overexpression of milR-87 enhanced disease severity, confirming that milR-87 is crucial for Foc virulence in the infection process. We furthermore identified FOIG_15013 (a glycosyl hydrolase-coding gene) as the direct target of milR-87 based on the expression of FOIG_15013-GFP fusion protein. The FOIG_15013 deletion mutant displayed similar phenotypes as the overexpression of milR-87, with a dramatic increase in the growth, conidiation and virulence. Transient expression of FOIG_15013 in Nicotiana benthamiana leaves activates the host defense responses. Collectively, this study documents the involvement of milRNAs in the manifestation of the devastating fungal disease in banana, and demonstrates the importance of milRNAs in the pathogenesis and other biological processes. Further analyses of the biosynthesis and expression regulation of fungal milRNAs may offer a novel strategy to combat devastating fungal diseases.

Construction of a lncRNA-associated competing endogenous RNA regulatory network after traumatic brain injury in mouse

Traumatic brain injury (TBI) is a major public health problem worldwide which causes high mortality and disability. Functioning as microRNA (miRNA) sponges, long non-coding RNA (lncRNA) regulates the expression of protein-coding genes in a competing endogenous RNA (ceRNA) network. However, the lncRNA-associated ceRNA in TBI remains unclear. In this study, we processed the raw SRR files of mice cortex samples of sham injury (n = 3) and TBI groups (n = 3) to count files. Then, the expression profiles of lncRNAs and mRNAs were identified, and 86 differentially expressed (DE) lncRNAs and 1201 DEmRNAs between sham and TBI groups were identified. The DEmRNAs were used to perform enrichment analyses. Next, a lncRNA-miRNA-mRNA regulatory ceRNA network was constructed. The network consisted of 23 mRNAs, 5 miRNAs and 2 lncRNAs. The expression alternations of the 5 miRNAs were validated via qRT-PCR. The subnetwork of hub lncRNA Neat1 was extracted. We identified a potential inflammatory associated regulatory axis: Neat1/miR-31-5p/Myd88 axis. The PPI network based on DEmRNA involved in ceRNA network was constructed PPI networks to identify the hub genes. Finally, DElncRNAs and DEmRNAs were selected randomly and validated by qRT-PCR. In conclusion, with the lncRNA-miRNA-mRNA ceRNA network provided above, we can improve our understanding of the regulatory mechanisms and interaction among lncRNAs, miRNAs and mRNAs in TBI process.

Congested Heart Failure in Small Breeds Dogs

Mitral valve disease, commonly known as MVD, is the most common heart disease in dogs, accounting for nearly 75% of all dogs affected. The characteristic of this predominant disease includes collagen degradation, elastic fiber fragmentation and proteoglycan accumulation, leading to deterioration of the mitral valve and ultimately, congestive heart failure (CHF). Treatment to reverse or even delay the damaging effects of MVD has not yet been discovered due to a lack of awareness of the underlying processes. Furthermore, this disease in dogs has many similarities with the human MVD and may potentially serve as a translational model for studying MVD further. Therefore, it is imperative to identify the causes and underlying mechanisms associated with canine MVD in order to treat these patients more efficiently at the earliest detectable stage. MicroRNAs (miRNAs) are small, 21‐25 nucleotides in length, non‐coding RNAs that can down‐regulate the expression of protein coding genes by binding to the 3’UTR sites in their messenger RNAs (mRNA), causing either degradation or gene silencing. Prior studies have shown that one miRNA may regulate multiple mRNAs, subsequently effecting the downstream levels of gene expression. Furthermore, if miRNAs prove to be a useful biomarker of heart disease, not only may they serve as detectors of early disease onset, but they may also be useful as therapeutic agents. Given this recent data, we propose to test the hypothesis that circulating miRNAs may be useful biomarkers for detection of CHF, secondary to MVD. Liquid biopsies (blood samples) were collected in EDTA tubes from 7 healthy dogs with no prior history of heart disease and 7 dogs being treated for CHF secondary to MVD. Total serum RNA was isolated using miRNeasy Serum/Plasma Kit (Qiagen). Isolated RNA was then reverse transcribed using miScript II RT Kit (Qiagen) and lastly, miRNA was quantified using miScript SYBR Green PCR Kit, along with miScript miRNA PCR Arrays (Qiagen).

LncRNA, miRNA and transcriptional co-regulatory network of breast and ovarian cancer reveals hub molecules

Our research focused on the development of a regulatory network of miRNA-lncRNA and miRNA-transcription factor associated with Breast Cancer (BC) and Ovarian Cancer (OC), utilising experimentally identified data from previous research works. The regulatory data from the target network helped in the identification of the most vital miRNA, lncRNA and transcription factor (TFs) hub molecules involved in the prognosis of BC and OC. Breast cancer is one of the leading types of cancer in the world whereas ovarian cancer is difficult to detect due to the lack of symptoms in the initial stages. lncRNAs are known to compete for miRNAs as per previous evidence shown in favour of the competing endogenous RNA theory. TFs are vital proteins that regulate the expression of protein coding genes. miRNAs have been known to be involved in post-transcriptional gene silencing. Thus miRNA-lncRNA interactions and miRNA-TF interactions should have a significant impact on the expression of different genes, the irregularity of which leads to diseases like cancer. Our work has revealed three lncRNAs: KCNQ1OT1, XIST and NEAT1 as well as two TFs: RELA and TP53 to have the most significant impact on both breast and ovarian cancer. We identified four miRNAs which had the maximum lncRNA targets, common to both cancers: hsa-mir-93-5p, hsa-mir-519d-3p, hsa-mir-106a-5p and hsa-mir-106b-5p. The top 15 miRNAs having maximum TF targets were found to be identical for both cancers.

Lrwd1 impacts cell proliferation and the silencing of repetitive DNA elements.

SummaryLRWD1, also known as ORCA, is a nuclear protein functioning in multiple biological processes. Using its WD40 domain LRWD1 interacts with repressive histone marks and maintains the silencing of heterochromatin regions in mammalian cells. ORCA also associates with the origin recognition complex (ORC) and facilitates prereplication complex formation at late‐replicating origins. However, whether LRWD1 plays a role during development and the functional significance of LRWD1 in vivo remains largely unknown. Using gene‐trap approach we generated Lrwd1 knockout mice and examined the expression of Lrwd1 during embryonic development. We found that Lrwd1 is ubiquitously expressed in the majority of the developing mouse embryo. Depletion of LRWD1 did not affect embryonic development but the postnatal growth of the homozygous mutants is retarded. In vitro cultured mouse embryonic fibroblasts (MEFs) depleted of LRWD1 displayed a reduced proliferation compared to wild type cells. We also showed that the knockout of Lrwd1 in MEFs increased the expression of the epigenetically silenced repetitive elements but with minimal effect on the expression of protein coding genes. Together, these results suggest that LRWD1 plays an important, but not essential, role in postnatal development by regulating cell proliferation likely through modulating DNA replication.

MicroRNAs in neural crest development and neurocristopathies.

The neural crest (NC) is a vertebrate-specific migratory population of multipotent stem cells that originate during late gastrulation in the region between the neural and non-neural ectoderm. This population of cells give rise to a range of derivatives, such as melanocytes, neurons, chondrocytes, chromaffin cells, and osteoblasts. Because of this, failure of NC development can cause a variety of pathologies, often syndromic, that are globally called neurocristopathies. Many genes are known to be involved in NC development, but not all of them have been identified. In recent years, attention has moved from protein-coding genes to non-coding genes, such as microRNAs (miRNA). There is increasing evidence that these non-coding RNAs are playing roles during embryogenesis by regulating the expression of protein-coding genes. In this review, we give an introduction to miRNAs in general and then focus on some miRNAs that may be involved in NC development and neurocristopathies. This new direction of research will give geneticists, clinicians, and molecular biologists more tools to help patients affected by neurocristopathies, as well as broadening our understanding of NC biology.

The Role of microRNAs in the Drosophila Melanogaster Visual System.

MicroRNAs (miRNAs) are a class of small non-coding RNAs (∼22 nucleotides in length) that negatively regulate protein-coding gene expression post-transcriptionally by targeting mRNAs and triggering either translational repression or RNA degradation. MiRNA genes represent approximately 1% of the genome of different species and it has been estimated that every miRNA can interact with an average of 200 mRNA transcripts, with peaks of 1,500 mRNA targets per miRNA molecule. As a result, miRNAs potentially play a fundamental role in several biological processes including development, metabolism, proliferation, and apoptotic cell death, both in physiological and pathological conditions. Since miRNAs were discovered, Drosophila melanogaster has been used as a model organism to shed light on their functions and their molecular mechanisms in the regulation of many biological and behavioral processes. In this review we focus on the roles of miRNAs in the fruit fly brain, at the level of the visual system that is composed by the compound eyes, each containing ∼800 independent unit eyes called ommatidia, and each ommatidium is composed of eight photoreceptor neurons that project into the optic lobes. We describe the roles of a set of miRNAs in the development and in the proper function of the optic lobes (bantam, miR-7, miR-8, miR-210) and of the compound eyes (bantam, miR-7, miR-9a, miR-210, miR-263a/b, miR-279/996), summarizing also the pleiotropic effects that some miRNAs exert on circadian behavior.

Insight Into the Long Noncoding RNA and mRNA Coexpression Profile in the Human Blood Transcriptome Upon Leishmania infantum Infection.

Visceral leishmaniasis (VL) is a vector-borne infectious disease that can be potentially fatal if left untreated. In Brazil, it is caused by Leishmania infantum parasites. Blood transcriptomics allows us to assess the molecular mechanisms involved in the immunopathological processes of several clinical conditions, namely, parasitic diseases. Here, we performed mRNA sequencing of peripheral blood from patients with visceral leishmaniasis during the active phase of the disease and six months after successful treatment, when the patients were considered clinically cured. To strengthen the study, the RNA-seq data analysis included two other non-diseased groups composed of healthy uninfected volunteers and asymptomatic individuals. We identified thousands of differentially expressed genes between VL patients and non-diseased groups. Overall, pathway analysis corroborated the importance of signaling involving interferons, chemokines, Toll-like receptors and the neutrophil response. Cellular deconvolution of gene expression profiles was able to discriminate cellular subtypes, highlighting the contribution of plasma cells and NK cells in the course of the disease. Beyond the biological processes involved in the immunopathology of VL revealed by the expression of protein coding genes (PCGs), we observed a significant participation of long noncoding RNAs (lncRNAs) in our blood transcriptome dataset. Genome-wide analysis of lncRNAs expression in VL has never been performed. lncRNAs have been considered key regulators of disease progression, mainly in cancers; however, their pattern regulation may also help to understand the complexity and heterogeneity of host immune responses elicited by L. infantum infections in humans. Among our findings, we identified lncRNAs such as IL21-AS1, MIR4435-2HG and LINC01501 and coexpressed lncRNA/mRNA pairs such as CA3-AS1/CA1, GASAL1/IFNG and LINC01127/IL1R1-IL1R2. Thus, for the first time, we present an integrated analysis of PCGs and lncRNAs by exploring the lncRNA–mRNA coexpression profile of VL to provide insights into the regulatory gene network involved in the development of this inflammatory and infectious disease.